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At least 1,171 records · Page 65Linked to original sources
PubMed2005

Insights into genotype-phenotype correlation in pachyonychia congenita from the human intermediate filament mutation database.

Keratins are the intermediate filament proteins specifically expressed by epithelial cells. The Human Genome Project has uncovered a total of 54 functional keratin genes that are differentially expressed in specific epithelial structures of the body, many of which involve the epidermis and its appendages. Pachyonychia congenita (PC) is a group of autosomal dominant genodermatoses affecting the nails, thick skin and other ectodermal structures, according to specific sub-type. The major clinical variants of the disorder (PC-1 and PC-2) are known to be caused by dominant-negative mutations in one of four differentiation-specific keratins: K6a, K6b, K16, and K17. A total of 20 human keratin genes are currently linked to single-gene disorders or are predisposing factors in complex traits. In addition, a further six intermediate filament genes have been linked to other non-epithelial genetic disorders. We have established a comprehensive mutation database that catalogs all published independent occurrences of intermediate filament mutations (http://www.interfil.org), with details of phenotypes, published papers, patient support groups and other information. Here, we review the genotype-phenotype trends emerging from the spectrum of mutations in these genes and apply these correlations to make predictions about PC phenotypes based on the site of mutation and keratin pair involved.

Age of Onset↗
PubMed2005

Mapping of 443 porcine EST improves the comparative maps for SSC1 and SSC7 with the human genome.

Numerous mapping studies of complex traits in the pig have resulted in quantitative trait loci (QTL) intervals of 10-20 cM. To improve the chances to identify the genes located in such intervals, increased expressed sequence tags (EST)-based marker density, coupled with comparative mapping with species whose genomes have been sequenced such as human and mouse, is the most efficient tool. In this study, we mapped 443 porcine EST with a radiation hybrid (RH) panel (384 had LOD > 6.0) and a somatic cell hybrid panel. Requiring no discrepancy between two-point and multipoint RH data allowed robust assignment of 309 EST, of which most were located on porcine chromosomes (SSC) 1, 4, 7, 8 and X. Moreover, we built framework maps for two chromosomes, SSC1 and SSC7, with mapped QTL in regions with known rearrangement between pig and human genomes. Using the Blast tool, we found orthologies between 407 of the 443 pig cDNA sequences and human genes, or to existing pig genes. Our porcine/human comparative mapping results reveal possible new homologies for SSC1, SSC3, SSC5, SSC6, SSC12 and SSC14 and add markers in synteny breakpoints for chromosome 7.

Animals↗
PubMed2006

Gene expression of cytokines and cytokine receptors is modulated by the common variability of the mitochondrial DNA in cybrid cell lines.

Some lines of evidence indicate that common polymorphisms of mitochondrial DNA (mtDNA) act as susceptibility factors in complex traits, such as age-related common diseases. There is also evidence that the cell capability to compensate ravages caused by intrinsic or extrinsic stress factors could contribute to some of these diseases. The cross-talk between nuclear and mitochondrial genome may link the above observations if we assume that the transcription of stress-responder nuclear genes is modulated according to the mtDNA common variability. Cytokines and cytokine receptors are key molecules in stress response. We could, therefore, check the above hypothesis by analyzing expression patterns of cytokine and cytokine receptor genes in response to stress in cell lines sharing the same nuclear genome but different mtDNA. By using a cybrid model (143B.TK- osteosarcoma cells depleted of their own mtDNA and repopulated with foreign mitochondria) we show that the transcription patterns of some of such genes are specifically modulated by the variability of the mitochondrial genome not only under stress conditions (interleukin-6) but also at basal conditions (interleukin-1beta and tumor necrosis factor receptor 2). These findings provide a first experimental evidence of a relationship between mtDNA common variability and expression pattern of stress responder nuclear genes in human cells.

Cell Fusion↗
PubMed2004

Nested core collections maximizing genetic diversity in Arabidopsis thaliana.

The successful exploitation of natural genetic diversity requires a basic knowledge of the extent of the variation present in a species. To study natural variation in Arabidopsis thaliana, we defined nested core collections maximizing the diversity present among a worldwide set of 265 accessions. The core collections were generated based on DNA sequence data from a limited number of fragments evenly distributed in the genome and were shown to successfully capture the molecular diversity in other loci as well as the morphological diversity. The core collections are available to the scientific community and thus provide an important resource for the study of genetic variation and its functional consequences in Arabidopsis. Moreover, this strategy can be used in other species to provide a rational framework for undertaking diversity surveys, including single nucleotide polymorphism (SNP) discovery and phenotyping, allowing the utilization of genetic variation for the study of complex traits.

Arabidopsis↗
PubMed1994

Apolipoprotein B gene polymorphisms in ischemic heart disease and hypercholesterolemia: effects of age and sex.

The association of polymorphic alleles of the apolipoprotein B gene (Insertion/Deletion-, XbaI-, MspI-, EcoRI-, and 3'-VNTR polymorphisms) with variation in lipid concentrations (total cholesterol (T-C), HDL cholesterol (HDL-C), and log-triglycerides (TG)) in plasma was studied in 259 men and 59 women with moderate hypercholesterolemia (T-C 5.5-8.0 mmol/l and TG < 2.5 mmol/l) and ischemic heart disease, especially in relation to the effect of sex and age. The XbaI and the Ins/Del polymorphic alleles were associated with variation in T-C, but only in patients below the 75th percentile for age. The XbaI and Ins/Del polymorphic alleles were synergistically associated with variation in T-C: the X+ and the Del alleles were associated with higher cholesterol concentrations. Younger male patients had the highest frequency of haplotypes including both the X+ and the Del alleles, but the most striking difference was a significantly higher frequency of haplotypes including both the X- and the Ins alleles in female and in older male patients. The heterogeneity of association of polymorphic alleles in the apolipoprotein B gene to complex traits like hypercholesterolemia and ischemic heart disease in this study could explain why in most studies the X+ allele has been associated with higher cholesterol levels, whereas the X- allele has been associated with symptomatic atherosclerosis. The results of our study emphasize the importance of age and sex in measured genotype association studies.

Adult↗
PubMed2005

Genetic basis of hearing loss associated with enlarged vestibular aqueducts in Koreans.

Sensorineural hearing loss associated with enlargement of the vestibular aqueduct (EVA) can be associated with mutations of the SLC26A4 gene. In western populations, less than one-half of the affected individuals with EVA have two mutant SLC26A4 alleles, and EVA is frequently caused by unknown genetic or environmental factors alone or in combination with a single SLC26A4 mutation as part of a complex trait. In this study, we ascertained 26 Korean probands with EVA and performed nucleotide sequence analysis to detect SLC26A4 mutations. All subjects had bilateral EVA, and 20 of 26 were sporadic (simplex) cases. Fourteen different mutations were identified, including nine novel mutations. Five mutations were recurrent and accounted for 80% of all mutant alleles, providing a basis for the design and interpretation of cost-efficient mutation detection algorithms. Two mutant alleles were identified in 21 (81%), one mutant allele was detected in three (11%), and zero mutant allele was detected in two (8%) of 26 probands. The high proportion of Korean probands with two SLC26A4 mutations may reflect a reduced frequency of other genetic or environmental factors causing EVA in comparison to western populations.

Adolescent↗
PubMed2005

An improved protocol for the production of AFLP markers in complex genomes by means of capillary electrophoresis.

The amplified fragment-length polymorphism (AFLP) technology is a recently introduced method to investigate genomes of different complexity, from microbial to higher organisms. It is applied to purposes as diverse as identification of species, strain and varieties, investigation of genetic diversity within and between populations, simple and complex trait mapping, and construction of linkage and physical maps. This technology has been designed on the use of primers labelled with radioactivity and on AFLP fragment separation on sequencing gel. We show that the original EcoRI/TaqI AFLP protocol does not perform appropriately when transferred to fluorescent labelling and capillary electrophoresis (CE), and propose an improved protocol for the production of high-quality AFLP markers in fish, rodents and artiodactyles by means of the Beckman-Coulter CEQ2000 automatic DNA sequencer. In addition, we describe the procedure routinely used in our laboratory to obtain binary matrices from AFLP profiles with the aid of Genographer free-share software (vers. 1.6.0, J.J. Benham, Montana State University), able to elaborate original fragment data and convert them to standard graphical formats for phylogenetic analyses. Comparison with radioactive AFLPs in goats confirmed the reliability of the protocol developed for CE. In fact, 107 fragments generated by two primer combinations and identified by both techniques were attributed the same scoring. Compared with traditional methods, the use of capillary systems and automated analysis increases data throughput and scoring reliability, decreasing the overall experimental error.

Animals↗
PubMed2005

Does weight loss prognosis depend on genetic make-up?

The prevalence of obesity is rising throughout the world. Indeed, obesity has reached epidemic proportions in many developed and transition countries. Obesity is a complex disease with multifactorial origin, which in many cases appears as a polygenic condition affected by environmental factors. Treatment or prevention of obesity is necessary to reverse or avoid the onset of type 2 diabetes and other obesity-related diseases. Weight loss is a complex trait that depends on many environmental, behavioural and genetic influences. An effective programme for the management of overweight and obesity must take into account all of these factors. Individual responses to weight loss interventions vary widely and reliable predictors of successful slimming are poorly understood. The individual genetic make-up participating in energy expenditure regulation, appetite control, lipid metabolism and adipogenesis, have been reported to affect the risk of treatment failure in some subjects. In addition, the genotype could also help to predict the changes in lipid profile, cardiovascular risk factors and insulin sensitivity in response to weight loss. Herein, the current evidence from human studies that support the existence of a genetic component and the participation of different polymorphisms in the prognosis of weight loss induced by interventions leading to a negative energy balance are reviewed.

Energy Metabolism↗
PubMed1989

Children's perceptions of peer reputations and their social reputations among peers.

The influence of social and cognitive developmental processes on the construction of social reputation was assessed by having first-, third-, and fifth-grade (mean age of 7-0, 8-11, and 10-11, respectively) boys and girls (N = 182), identified as to sociometric status, provide free descriptions of their classmates. These descriptions were aggregated by subject (descriptions made by a child) and by target (descriptions made about a child). Discriminant analyses revealed that rejected children were segregated from their peers by negative attitudes and peer ostracism; this social reputation was more distinct for older rejected children than younger rejected children. In contrast, neglected children were perceived in less distinctive reputational terms but, unlike rejected children, were notable for perceiving peers differently. Older children were more likely than younger children to describe the reputations of their peers with complex trait concepts. Sex differences included the following: rejected boys were perceived as having characteristics polar opposite to accepted qualities for girls, whereas rejected girls were perceived as having characteristics polar opposite to acceptable qualities for boys. The social implications of cognitive developmental change and the developmental implications of social differentiation among peers were discussed.

Child↗
PubMed1995

Genetic epidemiology of breast cancer: interest of survival analysis methods.

In an attempt to explain the controversy resulting from the analysis of the breast cancer data collected by Jacobsen, a segregation analysis was performed using successively the unified mixed model (UM) and the logistic hazard function model (LHM) (Abel & Bonney, 1990). Under the UM, age of onset of the disease cannot be taken into account, each individual being assigned to a liability class according to his age at examination, whereas, in the LHM, variable age of onset is modelled using survival analysis methods. Under the UM, we confirmed the results of Demenais et al. (1986b), i.e. the transmission probabilities are significantly different from Mendelian expectations. The same results were obtained when taking into account the specific mortality for the computation of the morbid risk observed in a given liability class. Under the LHM, the analysis provides evidence for a monogenic autosomal model with a rare dominant allele responsible for the disease, and transmission probabilities compatible with Mendelian expectations. This study shows that the rejection of the Mendelian transmission under the UM can be due to a violation of a constraint of this model (i.e. the probability of being and not being affected in a given liability class should sum to 1) when a specific mortality is induced by the disease as in breast cancer. Survival analysis methods avoid these problems by taking into account the onset of the disease as the failure time event and are more suitable when studying a complex trait such as breast cancer.

Breast Neoplasms↗
PubMed2005

A behavioural genomic analysis of DNA markers associated with general cognitive ability in 7-year-olds.

BACKGROUND: Five DNA markers (single-nucleotide polymorphisms, SNPs) have recently been found to be associated with general cognitive ability ('g') in a sample of 7414 7-year-old twins. These children have also been studied at 2, 3, 4, and 7 years of age on measures of cognitive and language development and behaviour problems; family environment was also assessed. METHODS: We used these data to conduct a behavioural genomic analysis of the five SNPs and a composite of them ('SNP set') that explored developmental, multivariate, and genotype-environment (GE) issues. RESULTS: The 'g' SNP set identified at 7 years yielded significant associations with 'g' as early as 2 years. In multivariate analyses at 7 years, the 'g' SNP set was more strongly associated with verbal than nonverbal ability and with reading more than mathematics performance. GE correlations were found between the SNP set for 'g' at 7 years and preschool proximal measures of the family environment (chaos and discipline) rather than distal measures (maternal education and father's occupational class), suggesting evocative rather than passive GE correlation. Significant GE interactions were found for discipline, education and occupation in which the association between the SNP set and 'g' at 7 years is stronger in low-risk environments. CONCLUSIONS: Although the effect sizes of the five SNP associations are very small, behavioural genomic analyses using a 'g' SNP set illustrate how developmental, multivariate and GE questions can be addressed as more DNA associations are identified for complex traits such as 'g'.

Child↗
PubMed2006

Obesity is associated with genetic variants that alter dopamine availability.

Human and animal studies have implicated dopamine in appetite regulation, and family studies have shown that BMI has a strong genetic component. Dopamine availability is controlled largely by three enzymes: COMT, MAOA and MAOB, and by the dopamine transporter SLC6A3, and each gene has a well-characterized functional variant. Here we look at these four functional polymorphisms together, to investigate how heritable variation in dopamine levels influences the risk of obesity in a cohort of 1150, including 240 defined as obese (BMI > or = 30). The COMT and SLC6A3 polymorphisms showed no association with either weight, BMI or obesity risk. We found, however, that both MAOA and MAOB show an excess of the low-activity genotypes in obese individuals (MAOA:chi2= 15.45, p = 0.004; MAOB:chi2= 8.05, p = 0.018). Additionally, the MAOA genotype was significantly associated with both weight (p = 0.0005) and BMI (p = 0.001). When considered together, the 'at risk genotype'--low activity genotypes at both the MAOA and MAOB loci--shows a relative risk for obesity of 5.01. These results have not been replicated and, given the experience of complex trait genetics, warrant caution in interpretation. In implicating both the MAOA and MOAB variants, however, this study provides the first indication that dopamine availability (as opposed to other effects of MAOA) is involved in human obesity. It is therefore a priority to assess the associations in replication datasets.

Body Mass Index↗
PubMed2006

Susceptibility of biallelic haplotype and genotype frequencies to genotyping error.

With the availability of fast genotyping methods and genomic databases, the search for statistical association of single nucleotide polymorphisms with a complex trait has become an important methodology in medical genetics. However, even fairly rare errors occurring during the genotyping process can lead to spurious association results and decrease in statistical power. We develop a systematic approach to study how genotyping errors change the genotype distribution in a sample. The general M-marker case is reduced to that of a single-marker locus by recognizing the underlying tensor-product structure of the error matrix. Both method and general conclusions apply to the general error model; we give detailed results for allele-based errors of size depending both on the marker locus and the allele present. Multiple errors are treated in terms of the associated diffusion process on the space of genotype distributions. We find that certain genotype and haplotype distributions remain unchanged under genotyping errors, and that genotyping errors generally render the distribution more similar to the stable one. In case-control association studies, this will lead to loss of statistical power for nondifferential genotyping errors and increase in type I error for differential genotyping errors. Moreover, we show that allele-based genotyping errors do not disturb Hardy-Weinberg equilibrium in the genotype distribution. In this setting we also identify maximally affected distributions. As they correspond to situations with rare alleles and marker loci in high linkage disequilibrium, careful checking for genotyping errors is advisable when significant association based on such alleles/haplotypes is observed in association studies.

Alleles↗
PubMed2002

Vacuolar H(+)-ATPase, but not mitochondrial F(1)F(0)-ATPase, is required for NaCl tolerance in Saccharomyces cerevisiae.

Salt tolerance in Saccharomyces cerevisiae is a complex trait, involving regulation of membrane polarization, Na(+) efflux and sequestration of Na(+) in the vacuole. Since transmembrane transport energized by H(+)-adenosine triphosphatases (ATPases) is common to all of these tolerance mechanisms, the objective of this study was to characterize the responses of the plasma membrane H(+)-ATPase, vacuolar H(+)-ATPase and mitochondrial F(1)F(0)-ATPase to NaCl stress. We hypothesized that since the vacuolar ATPase is responsible for generating the proton motive force required for import of cations (such as Na(+)) into the vacuole, strains lacking this activity should be hypersensitive to NaCl. We found that strains lacking vacuolar ATPase activity were in fact hypersensitive to NaCl, while strains lacking ATP synthase were not. This effect was specific to the ionic component of NaCl stress, since the mutant strains were indistinguishable from wild-type and complemented strains in the presence of sorbitol.

Mitochondrial Proton-Translocating ATPases↗
PubMed2005

Characterization of the parallel rod floor apparatus to test motor incoordination in mice.

Impairment of motor coordination, or ataxia, is a prominent effect of alcohol ingestion in humans. To date, many models have been created to examine this phenomenon in animals. Evidence suggests that the tasks thought to measure this behavior in mice actually measure different components of this complex trait. We have characterized the parallel rod floor apparatus to quantify ethanol-induced motor incoordination. Using genetically heterogeneous mice, we evaluated the influence of rod diameter and inter-rod distance on dose-related ethanol-induced motor incoordination to select parameters that optimized testing procedures. We then used the DBA/2J and C57BL/6J inbred strains of mice to examine the effect of 2 g/kg of ethanol, by serially testing mice on two floor types, separated by 1 week. Finally, we tested eight inbred strains of mice on four floor types to examine patterns of strain sensitivity to 2 g/kg of intraperitoneal ethanol and determined the test parameters that maximized strain effect size. Motor incoordination varied depending on the floor type and strain. When data from strain 129S1/SvlmJ were removed from the analyses because of their extreme behavior, the greatest strain effect size was observed on one floor type during the first 10 min of testing after 2 g/kg of intraperitoneal ethanol. These findings suggest that the parallel rod floor apparatus provides a useful means for examining ethanol-induced motor incoordination in mice but that specific testing procedures are important for optimizing detection of motor incoordination and genetic influences.

Animals↗
PubMed2007

Investigating the role of brain-derived neurotrophic factor in relapsing-remitting multiple sclerosis.

Multiple sclerosis (MS) is a common, heterogeneous disorder of the central nervous system with a complex trait composed of both genetic and environmental factors. Recently, scientific interest has increased in defining factors that possibly contribute to brain functional plasticity; the results might be useful to assess the relationship between MS lesion burden and clinical events, as well as explaining the well-known phenotypic heterogeneity of the disease. In this study, we explored the effect of the Val66Met brain-derived neurotrophic factor (BDNF) functional polymorphism on cognitive performances and volumetric measurements obtained by magnetic resonance imaging of the brain in a selected population of relapsing-remitting MS (RRMS) patients, with relatively short disease duration and minimal clinical disability, compared to gender, age and educational-level matched healthy subjects. We found that in the RRMS group, the BDNF Met-allele was significantly associated with the lower volume of cerebral grey matter (GM) (P = 0.005). Furthermore, a significant (P = 0.013) interaction effect between 'MS-status' and the BDNF genotype was found for GM volumes, with the result that patients carrying the BDNF Met-allele showed a higher risk of developing global GM atrophy than the homozygous Val/Val. No BDNF-related impact on global neuropsychological functions resulted in either RRMS patients or controls. Our data seem to be consistent with the reported influence of BDNF in neuronal plasticity, thus suggesting that the Met-allele might have a negative prognostic effect on cortical morphometry in RRMS patients.

Adolescent↗
PubMed2000

Variability in phenotypic traits in core and peripheral populations of wild barley Hordeum spontaneum Koch.

Populations of wild barley, H. spontaneum Koch., were collected in two countries, Israel and Turkmenistan, in environments representing two similar sharp clines of aridity. This allowed us to use the same criteria to define species core and periphery in two regions. Plants from 10 Israeli and 19 Turkmenian populations were grown in a field trial with three water treatments and compared for amount and structure of variation in phenological and morphological traits. Extent of variation was similar in populations at species border (periphery by aridity criterion) or at species border and near it (by habitat), and in populations inhabiting favorable environments away from the border (core). In contrast, two regions (Israel and Turkmenistan) exhibited different amount of variation in phenotypic traits. Israeli populations were more diverse than Turkmenian populations in all except one phenotypic traits and the variation was differently structured among regionally specific core and periphery. While Turkmenian core and periphery defined by either criterion did not differ for all except one trait, corresponding Israeli populations exhibited opposite patterns of variation for trait complexes. Israeli core (Mediterranean) populations were twice as variable than peripheral (desert) populations in parameters of reproductive growth (stem, spike and awn length) and grain filling (spikelet weight) and half as variable in the length of flag and penultimate leaves and onset of reproduction. Possible modes of regionally specific natural selection as a cause of regional/local variation in phenotypic triats are discussed.

Founder Effect↗
PubMed2000

Inflamm-aging. An evolutionary perspective on immunosenescence.

In this paper we extend the "network theory of aging," and we argue that a global reduction in the capacity to cope with a variety of stressors and a concomitant progressive increase in proinflammatory status are major characteristics of the aging process. This phenomenon, which we will refer to as "inflamm-aging," is provoked by a continuous antigenic load and stress. On the basis of evolutionary studies, we also argue that the immune and the stress responses are equivalent and that antigens are nothing other than particular types of stressors. We also propose to return macrophage to its rightful place as central actor not only in the inflammatory response and immunity, but also in the stress response. The rate of reaching the threshold of proinflammatory status over which diseases/disabilities ensue and the individual capacity to cope with and adapt to stressors are assumed to be complex traits with a genetic component. Finally, we argue that the persistence of inflammatory stimuli over time represents the biologic background (first hit) favoring the susceptibility to age-related diseases/disabilities. A second hit (absence of robust gene variants and/or presence of frail gene variants) is likely necessary to develop overt organ-specific age-related diseases having an inflammatory pathogenesis, such as atherosclerosis, Alzheimer's disease, osteoporosis, and diabetes. Following this perspective, several paradoxes of healthy centenarians (increase of plasma levels of inflammatory cytokines, acute phase proteins, and coagulation factors) are illustrated and explained. In conclusion, the beneficial effects of inflammation devoted to the neutralization of dangerous/harmful agents early in life and in adulthood become detrimental late in life in a period largely not foreseen by evolution, according to the antagonistic pleiotropy theory of aging.

Aging↗